On Kawauchi Region on mouth of Yoshino River in Japan, which used to be a wetland, farm land has been developed by land reclamation. In this region, rice, lotus root and sweet potato are mainly cultivated. However because of the high salt concentration in groundwater due to seawater intrusion, crops are subjected to damage by salt. Especially in the paddy fields and lotus fields, salinity damage could be serious because of the fine texture of the soil and flooding surplus water for salt removal is practiced. To establish the most efficient management of irrigation water, water demand including water for salt removal has to be known. So in this study, we investigated the possibility of salinity damage in the fields by the measurement of electrical conductivity (EC) at a number of points that were considered to be critical for water quality management and the spatial distribution of EC was predicted with geostatistical analysis. The EC value in the groundwater was high in the area near the riparian and, in such areas surplus water for the salt removal was considered necessary. On the other hand, there were areas in paddy fields and lotus fields where the EC in the surface water was high regardless of the distance from the river. In such areas, irrigation water might contain salt and management of irrigation water had to be improved. By linking the prediction values of EC with the database of each plot, it is possible to propose methods for efficient water management and effective quality control of crops in a form that is easily understood by farmers.